Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho Bleekeri) using genome‐wide SNP markers

Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF‐seq)‐based genotyping was performed for Sichuan taimen with 43 yearling individuals from three locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome‐wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (2.6 × 10^?3 ± 0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < .001), and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic‐relatedness‐guided breeding and conservation strategy for wild fish species without pedigree information records.     

Down-regulation of RBP4 indicates a poor prognosis and correlates with immune cell infiltration in hepatocellular carcinoma

Recent research has indicated that metabolically related genes play crucial roles in the pathogenesis of hepatocellular carcinoma (HCC). We evaluated the associations between novel biomarkers and retinol-binding protein 4 (RBP4) for predicting clinical HCC outcomes, hub-related genes, pathway regulation, and immune cells infiltration. Bioinformatic analyses based on data from The Cancer Genome Atlas were performed using online analysis tools. RBP4 expression was low in HCC and was also down-regulated in pan-cancers compared with normal tissues. RBP4 expression was also significantly different based on age (41–60 years old versus 61–80 years old), and low RBP4 expression levels were associated with advanced tumor stages and grades. Higher RBP4 expression was associated with better overall survival time in HCC patients, and we identified a deletion-mutation rate of 1.4% in RBP4. We also identified ten co-expressed genes most related to RBP4 and explored the relationships between six hub genes (APOB, FGA, FGG, SERPINC1, APOA1, and F2) involved in RBP4 regulation. A pathway enrichment analysis for RBP4 indicated complement and coagulation cascades, metabolic pathways, antibiotic biosynthesis pathways, peroxisome proliferator-activated receptor signaling pathways, and pyruvate metabolism pathways. These results suggest that RBP4 may be a novel biomarker for HCC prognosis, and an indicator of low immune response to the disease.     

Antifungal Effect of Long Noncoding RNA 9708-1 in the Vulvovaginal Candidiasis Murine Model

Mycopathologia - Vulvovaginal candidiasis (VVC) caused by Candida spp. affects 70–75% of women at least once during their lives. We aim to elucidate the potential mechanism of VVC and...     

An efficient Oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae

A chromosome-specific painting technique has been developed which combines the most recent approaches of the companion disciplines of molecular cytogenetics and genome research. We developed seven oligonucleotide (oligo) pools derivd from single-copy sequences on chromosomes 1 to 7 of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The seven groups of pooled oligos comprised between 10 986 and 12 496 45-bp monomers, and these then produced stable fluorescence in situ hybridization (FISH) signals on chromosomes of each linkage group of wheat and barley. The pooled oligo probes were applied to high-throughput karyotyping of the chromosomes of other Triticeae species in the genera Secale, Aegilops, Thinopyrum, and Dasypyrum, and the study also extended to some wheat-alien amphiploids and derived lines. We demonstrated that a complete set of whole-chromosome oligo painting probes facilitated the study of inter-species chromosome homologous relationships and visualized non-homologous chromosomal rearrangements in Triticeae species and some wheat-alien species derivatives. When combined with other non-denaturing FISH procedures using tandem-repeat oligos, the newly developed oligo painting techniques provide an efficient tool for the study of chromosome structure, organization, and evolution among any wild Triticeae species with non-sequenced genomes.     

Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants

Evidence is emerging that t RNA-derived fragments(t RFs) are regulatory molecules. Studies of t RFs in plants have been based on conventional small RNA sequencing, and focused on profiling of t RF-5 and t RF-3 species. A more comprehensive and quantitative analysis of the entire t RF population is highly necessary. Here, we employ t RNA-seq and YAMAT-seq, and develop a bioinformatics tool to comprehensively profile the expressions of t RNAs and t RFs in plants. We show that in Arabidopsis,approximately half of t RNA genes are extremely weakly expressed, accounting for only 1% of total t RNA abundance, while～12% of t RNA genes contribute to ～80% of t RNA abundance. Our t RNA sequencings in various plants reveal that t RNA expression profiles exhibit a cross-species conserved pattern. By characterizing the composition of a highly heterogeneous t RF population, we show that t RNA halves and previously unnoticed 10–16-nt tiny t RFs represent substantial portions. The highly accumulated 13-nt and 16-nt tiny t RFs in Arabidopsis indicate that tiny t RFs are not random t RNA degradation products. Finally,we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of t RNAs and t RFs in the model plants Arabidopsis and rice.     

A dynamic task scheduler tolerant to multiple hibernations in cloud environments

Cluster Computing - Cloud platforms usually offer several types of Virtual Machines (VMs) with different guarantees in terms of availability and volatility, provisioning the same resource through...     

Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum

Functional & Integrative Genomics - Growth is one of the most important traits of aquaculture breeding programs. Understanding the mechanisms underlying growth differences between individuals...     

A review of the botany,traditional uses,phytochemistry and pharmacology of Nepeta tenuifolia Briq.

Phytochemistry Reviews - Nepeta tenuifolia (N. tenuifolia) is a common aromatic herb that is widespread in East Asia. The aerial parts and spikes can be used as the traditional phytomedicines for...     

Association of FcRn Heavy Chain Encoding Gene (FCGRT) Polymorphisms with IgG Content in Bovine Colostrum

In this study, we evaluated haplotypes of the bovine FCGRT (encoding the FcRn heavy chain) and their relationship to the IgG concentration in bovine colostrum. Four single nucleotide polymorphism (SNP), classified into five haplotypes, were identified in a total of 49 Holstein-Frisians cows. Haplotype 5 was found to be significantly associated with a high IgG level ([OR] = 9.90, 95%CI = 1.11–88.34, p = 0.016) and haplotype 2 exhibited a similar trend ([OR] = 2.89, 95%CI = 1.17–7.11, p = 0.019).